Merge doxygen2 into develop (#553)

* Fixed warnings and started H5Epublic.h.

* Include H5FD* headers to correctly resolve references.

* Doxygen2 (#330)

* H5Eauto_is_v2.

* Added a few more calls.

* Added a few more H5E calls.

* First cut of H5E v2.

* Added the deprecated v1 calls.

* Updated spacing.

* Once more.

* Taking some inspiration from Eigen3.

* Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pen… (#352)

* Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pencode1, H5Pget_filter_by_id1,H5Pget_version, H5Pset_file_space,H5Pget_file_space. Someone already adds H5Pget_filter1. Also fixs an extra parameter 'close' call back function for HPregister2.

* doxygen work. fixs format by using clang-format.

* doxgen work for H5Pregister1 etc. Addressed Barbara and Gerd's comments.
For Quincey's comments, since we are not supposed to change the source code.
I leave this to future improvements.

* added documentation for H5P APIs (#350)

* add documenation for H5Pget_buffer,H5Pget_data_transform,H5Pget_edc_check,H5Pget_hyper_vector_size,H5Pget_preserve,H5Pget_type_conv_cb,H5Pget_vlen_mem_manager,H5Pset_btree_ratios

* format corrections

* fixed grammer

* fixed herr_t

* Better name.

* A fresh look.

* add doxygen to H5Ppublic.h

* use attention instead of warning

* Add doxygen comments in H5Ppublic.h (#375)

* Add doxygen comments in H5Ppublic.h

* H5Pset_meta_block_size
* H5Pset_metadata_read_attempts
* H5Pset_multi_type
* H5Pset_object_flush_cb
* H5Pset_sieve_buf_size
* H5Pset_small_data_block_size
* H5Pset_all_coll_metadata_ops
* H5Pget_all_coll_metadata_ops

* Add DOXYGEN_EXAMPLES_DIR to src/CMakeLists.txt

* Fix clang-format errors

* Fix filenames in doxygen/examples

* add doxygen to H5Ppublic.h (#378)

* add doxygen to H5Ppublic.h

* use attention instead of warning

Co-authored-by: Kimmy Mu <kmu@hdfgroup.org>

* Revert "add doxygen to H5Ppublic.h (#378)"

This reverts commit 2ee1821b138a5c00b15ea57ce9e950367480f5f2.

* Updated Doxygen variables.

* I forgot to copy two images.

* Enable desktop search by default.

* Add my assigned Doxygen documentation.

* Remove whitespace at EOL.  Appease clang-format.

* Addressed Chris' comments.

* Added an alias for asynchronous functions.

* One space is enough for all of us.

* Slightly restructured RM page.

* address some issues

* reformatting

* Style external links.

* reformatting

* reformatting

* Added "Metadata Caching in HDF5" as a technical note example.

* Revise this soon!

* Added specification examples.

* Fixed references.

* Added H5AC cache image stuff and file format study.

* Added older FMT versions. Where did 1.0 go?

* Updated C/C++ note and replaced ambiguous labels.

* Reformat source with clang v10.0.1.

* Added the VFL technical note.

* Added what I believe might be called version 1.0 of the format.

* Added the remaining specs.

* Added H5Z callback documentation and fixed a few mistakes.

* Added dox for deprecated H5G calls and fixed a few snippet blockIDs.

* clang-format happy?

* Ok?

* Bonus track: Deprecated H5D functions.

* Carry over the more detailed group description.

* Added documentation for the missing and deprecated H5R calls.

* Life is easier and less repetitive w/ snippets. Use them!

* Eliminate the snippet block ID artifacts in the HTML rendering.

* Fixed snippet HTML artifacts and added a few missing calls.

* Under 20 H5Ps to go!

* Almost complete!

* "This is a form of pedantry up with which I will not put." (Churchill)

* Let's not waste as much space on bulleted lists!

* First complete (?) draft of the Doxygen-based RM.

* Completeness check and minor fixes along the way.

* Pedantry.

* Adding missing H5FD calls checkpoint.

* Pedantry.

* More pedantry.

* Added H5Pset_fapl_log.

* First draft of H5ES.

* Fixed warnings.

* Prep. for map module.

* First cut of the map module.

* Pedantry.

* Possible H5F introduction.

* Fix the indentation.

* Pedantry.

* Ditto.

* Thanks to the reviewers for their comments.

* Added missing images.

* Line numbers are a distraction here.

* More examples, references, and clean-up. Don't repeat yourself!

* Clang pedantry.

* Ditto.

* More reviewer comments...

* Templatized references and cleaned up \todos.

* Committing clang-format changes

* Fixed MANIFEST.

* Addressed Quincey's comments. (OCPLs)

* Fixed a few more \todo items.

* Fixed more \todo items.

* Added attribute life cycle.

* Forgot the examples file.

* Committing clang-format changes

* Pedantry.

* Live and learn!

* Added a sample H5D life cycle.

* Committing clang-format changes

* Pedantry.

Co-authored-by: kyang2014 <kyang2014@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Kimmy Mu <kmu@hdfgroup.org>
Co-authored-by: Christopher Hogan <ChristopherHogan@users.noreply.github.com>
Co-authored-by: jya-kmu <53388330+jya-kmu@users.noreply.github.com>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

1 files changed, 251 insertions, 0 deletions

diff --git a/doxygen/hdf5doxy.css b/doxygen/hdf5doxy.css
new file mode 100644
index 0000000..8c03860
--- /dev/null
+++ b/doxygen/hdf5doxy.css
@@ -0,0 +1,251 @@
+
+/******** HDF5 specific CSS code ************/
+
+/**** Styles removing elements ****/
+
+/* remove the "modules|classes" link for module pages (they are already in the TOC) */
+div.summary {
+  display:none;
+}
+
+/* remove */
+div.contents hr {
+  display:none;
+}
+
+/**** ****/
+
+p, dl.warning, dl.attention, dl.note
+{
+  max-width:60em;
+  text-align:justify;
+}
+
+li {
+  max-width:55em;
+  text-align:justify;
+}
+
+img {
+  border: 0;
+}
+
+div.fragment {
+  display:table; /* this allows the element to be larger than its parent */
+  padding: 0pt;
+}
+pre.fragment {
+  border: 1px solid #cccccc;
+
+  margin: 2px 0px 2px 0px;
+  padding: 3px 5px 3px 5px;
+}
+
+/* Common style for all HDF5's tables */
+
+table.example, table.manual, table.manual-vl, table.manual-hl {
+    max-width:100%;
+    border-collapse: collapse;
+    border-style: solid;
+    border-width: 1px;
+    border-color: #cccccc;
+    font-size: 1em;
+
+    box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+    -moz-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+    -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+}
+
+table.example th, table.manual th, table.manual-vl th, table.manual-hl th {
+  padding: 0.5em 0.5em 0.5em 0.5em;
+  text-align: left;
+  padding-right: 1em;
+  color: #555555;
+  background-color: #F4F4E5;
+
+  background-image: -webkit-gradient(linear,center top,center bottom,from(#FFFFFF), color-stop(0.3,#FFFFFF), color-stop(0.30,#FFFFFF), color-stop(0.98,#F4F4E5), to(#ECECDE));
+  background-image: -moz-linear-gradient(center top, #FFFFFF 0%, #FFFFFF 30%, #F4F4E5 98%, #ECECDE);
+  filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#FFFFFF', endColorstr='#F4F4E5');
+}
+
+table.example td, table.manual td, table.manual-vl td, table.manual-hl td {
+  vertical-align:top;
+  border-width: 1px;
+  border-color: #cccccc;
+}
+
+/* header of headers */
+table th.meta {
+  text-align:center;
+  font-size: 1.2em;
+  background-color:#FFFFFF;
+}
+
+/* intermediate header */
+table th.inter {
+  text-align:left;
+  background-color:#FFFFFF;
+  background-image:none;
+  border-style:solid solid solid solid;
+  border-width: 1px;
+	border-color: #cccccc;
+}
+
+/** class for example / output tables **/
+
+table.example {
+}
+
+table.example th {
+}
+
+table.example td {
+  padding: 0.5em 0.5em 0.5em 0.5em;
+  vertical-align:top;
+}
+
+/* standard class for the manual */
+
+table.manual, table.manual-vl, table.manual-hl {
+    padding: 0.2em 0em 0.5em 0em;
+}
+
+table.manual th, table.manual-vl th, table.manual-hl th {
+  margin: 0em 0em 0.3em 0em;
+}
+
+table.manual td, table.manual-vl td, table.manual-hl td {
+  padding: 0.3em 0.5em 0.3em 0.5em;
+  vertical-align:top;
+  border-width: 1px;
+}
+
+table.manual td.alt, table.manual tr.alt, table.manual-vl td.alt, table.manual-vl tr.alt {
+  background-color: #F4F4E5;
+}
+
+table.manual-vl th, table.manual-vl td, table.manual-vl td.alt {
+  border-color: #cccccc;
+  border-width: 1px;
+  border-style: none solid none solid;
+}
+
+table.manual-vl th.inter {
+  border-style: solid solid solid solid;
+}
+
+table.manual-hl td {
+  border-color: #cccccc;
+  border-width: 1px;
+  border-style: solid none solid none;
+}
+
+table td.code {
+  font-family: monospace;
+}
+
+h2 {
+  margin-top:2em;
+  border-style: none none solid none;
+  border-width: 1px;
+  border-color: #cccccc;
+}
+
+/**** Table of content in the side-nav ****/
+
+
+div.toc {
+  margin:0;
+  padding: 0.3em 0 0 0;
+  width:100%;
+  float:none;
+  position:absolute;
+  bottom:0;
+  border-radius:0px;
+  border-style: solid none none none;
+  max-height:50%;
+  overflow-y: scroll;
+}
+
+div.toc h3 {
+  margin-left: 0.5em;
+  margin-bottom: 0.2em;
+}
+
+div.toc ul {
+  margin: 0.2em 0 0.4em 0.5em;
+}
+
+span.cpp11,span.cpp14,span.cpp17 {
+  color: #119911;
+  font-weight: bold;
+}
+
+.newin3x {
+  color: #a37c1a;
+  font-weight: bold;
+}
+
+div.warningbox {
+  max-width:60em;
+  border-style: solid solid solid solid;
+  border-color: red;
+  border-width: 3px;
+}
+
+/**** old HDF5's styles ****/
+
+
+table.tutorial_code td {
+  border-color: transparent; /* required for Firefox */
+  padding: 3pt 5pt 3pt 5pt;
+  vertical-align: top;
+}
+
+
+/* Whenever doxygen meets a '\n' or a '<BR/>', it will put
+ * the text containing the character into a <p class="starttd">.
+ * This little hack together with table.tutorial_code td.note
+ * aims at fixing this issue. */
+table.tutorial_code td.note p.starttd {
+  margin: 0px;
+  border: none;
+  padding: 0px;
+}
+
+div.eimainmenu {
+  text-align:     center;
+}
+
+/* center version number on main page */
+h3.version {
+  text-align:     center;
+}
+
+
+td.width20em p.endtd {
+  width:  20em;
+}
+
+/* needed for huge screens */
+.ui-resizable-e {
+  background-repeat: repeat-y;
+}
+
+/* Style external links -- nav-tree is different */
+
+#nav-tree .label a {
+  padding:2px 16px 2px 2px;
+}
+
+a {
+  outline: none;
+  text-decoration: none;
+  padding: 2px 1px 0;
+}
+
+a[href*="http"] {
+  background: url('https://mdn.mozillademos.org/files/12982/external-link-52.png') no-repeat 100% 0;
+  background-size: 12px 12px;
+  padding-right: 16px;
+}